The Trump administration has withdrawn a piece of federal guidance requiring transgender students to have unfettered access to bathrooms and locker rooms matching their gender identity, in a move that could embolden many schools to restrict trans rights.

In doing so, the administration has signaled that it does not necessarily interpret current federal civil rights protections as prohibiting discrimination based on gender identity.

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A joint letter released by the departments of justice and education on Wednesday cited the legal battle on this question as justification for rescinding the guidance, “in order to further and more completely consider the legal issues involved”.

“In addition, the Departments believe that … there must be due regard for the primary role of the States and local school districts in establishing education policy,” the letter added.

The Obama administration issued the guidance in May 2016, in response to growing confusion and controversy over how schools should accommodate transgender students. The letter released on Wednesday left one major piece of that guidance intact: a recognition that schools bear some responsibility to prevent bullying and harassment of transgender students.

“This is a mean-spirited attack on hundreds of thousands of students who simply want to be their true selves and be treated with dignity while attending school,” said Mara Keisling, executive director of the National Center for Transgender Equality. “These young people already face incredible hurdles in their pursuit of education and acceptance. With a pen stroke, the Trump administration effectively sanctions the bullying, ostracizing, and isolation of these children, putting their very lives in danger.”

Opponents of such a change also argued that the impact of the announcement would be blunted by existing law. The administration, they argued, does not have the authority to revoke rights that have been recognised several times in the federal courts.

“Rescinding the guidance does not change the rights of students under Title IX [the federal law prohibiting sex discrimination in education and activities],” Chase Strangio, a staff attorney for the American Civil Liberties Union, wrote on Tuesday. “Trans students are protected from discrimination by federal law and the administration can’t change that.”

That argument is the subject of a forthcoming supreme court case. On 28 March, lawyers for Gavin Grimm, a Virginia high school student, will contend that federal laws against sex discrimination extend to bias against transgender people. Grimm claims his school is discriminating against him by refusing to allow him access to the boys’ bathroom.

Several federal appeals courts have already ruled that discriminating against transgender people based on their gender identity is a violation of federal law. In 2016, the fourth circuit court of appeals ruled in Grimm’s favor.

“We’re confident that the law is on Gavin’s side and he will prevail just as he did in the fourth circuit,” said Joshua Block, an ACLU attorney and the lead attorney for Grimm’s case. The ACLU argued that the move Wednesday would not impact Grimm’s case because it began before the guidance came out.

David Dinielli, deputy legal director for the Southern Poverty Law Center, said in a statement that by rescinding the guidance “the administration has contributed to the baseless hysteria and panic that puts so many vulnerable transgender youth at risk”.

The White House’s expected move comes one week after Jeff Sessions, the newly appointed attorney general, quietly withdrew the Department of Justice’s participation in the Obama guidance’s legal defence. More than20 states have challenged the guidance, which applies to all federally funded public schools, in federal court, and the guidance has been blocked by a federal judge. The justice department is no longer asking for a stay of that judge’s decision.

Sessions, who has long been hostile to LGBT rights, reportedly fought for Wednesday’s order over the objections of Betsy DeVos, the new education secretary. The report, by the New York Times, claimed that DeVos asked to preserve protections for students against bullying but was overruled by the president, who sided with his attorney general.

The joint letter from her agency and Sessions released on Wednesday read: “All schools must ensure that all students, including LGBT students, are able to learn and thrive in a safe environment. The Department of Education Office of Civil Rights will continue its duty under law to hear all claims of discrimination and will explore every opportunity to protect all students.”

White House press secretary Sean Spicer insisted on Wednesday that DeVos was onboard.

“The conclusions, everyone in the administration is agreed upon,” he told reporters. “There’s no daylight between anybody, between the president and any of the secretaries. I think there’s been some discussion between the timing of the issuance and recommendations or the exact wording.”

But on Wednesday, a tweet from Devos suggested otherwise:

Betsy DeVos (@BetsyDeVosED)

I consider protecting all students, including #LGBTQ students, not only a key priority for the Department, but for every school in America.

On the campaign trail, Donald Trump seldom mentioned transgender issues and has even, to the irritation of many LGBT advocates, styled himself as an LGBT ally. In April, he said a transgender person should “use the bathroom they feel is appropriate” and agreed that the transgender celebrity Caitlyn Jenner could use any bathroom she chose at Trump Tower in New York.

But advocates for LGBT rights have nevertheless been bracing themselves. Mike Pence, the vice-president, used his very first post-election interview to hint that the Trump administration would reverse Obama’s policies on transgender students.

“Washington has no business intruding on the operation of our local schools,” Pence said, in an interview he gave to the arch-conservative radio host James Dobson.

Access to gendered facilities is just one flashpoint in a far-reaching clash over transgender rights. This month, lawmakers in South Dakota considered a bill to give adoption workers broad authority to deny adoptions to LGBT parents. Oklahoma considered legislation permitting discrimination against gay and trans people by adoption agencies and private businesses.

But LGBT advocates and a growing number of medical and mental health experts have argued that denying a trans person access to bathrooms and locker rooms can have serious negative effects, especially if that person is young.

“For transgender students, being in a school that affirms and supports their gender identity is critical to ensuring that they too can experience adolescence in a healthy and constructive manner,” reads one brief, by leading medical societies, in support of Grimm’s lawsuit. “Refusing to respect and affirm a transgender student’s gender identity communicates a clear, negative message: there is something wrong with the student that warrants this unequal treatment.”

States that are suing to block the guidance have called it an intrusion of the federal government and a threat to the bodily privacy of students who are not transgender.

LGBT advocates say there is no evidence of transgender-inclusive policies causing privacy invasions for other students.

James Esseks, director of the ACLU’s LGBT litigation, said in May: “There have been no disruptions, increases in public safety incidents, nor invasions of privacy related to protections for transgender people. While the Obama administration is being sued, the real targets here are vulnerable young people and adults who simply seek to live their lives free from discrimination when they go to school, work or the restroom.”